Amphibians play an important role in ecosystems and are one of the most threatened taxa worldwide. In order to protect their populations, it is essential to understand the factors affecting their distribution, abundance and diversity. Baixo Vouga Lagunar is a heterogeneous, human-modified, coastal wetland in north-west Portugal, with seasonal or permanently flooded habitats. We characterised the patterns of distribution, abundance and diversity of amphibians and aimed to identify its environmental drivers. Species richness was best explained by distance to the nearest well, followed by presence of temporary water bodies. Distance to the nearest well was also the most important driver of the composition of local amphibian assemblages, followed by the distance to forested areas. Our results reflect the findings of other studies in the Mediterranean region that have revealed the importance of seasonally available habitats, and stress the need for conservation of natural as well as artificial water bodies and traditional agricultural practices which promote a mosaic of amphibian habitats.